{"database": "metadata", "table": "run_metadata", "rows": [[67133, "SRR17097011", "SRX13284816", "SRS11197573", "SRP348912", "PRJNA785573", "Identifying key events from Per  and Polyfluoroalkyl Substances exposure that influence larval zebrafish in light:dark assay using RNA sequencing analysis of perfluorohexane 1 sulfonate PFHxS", "GSE190009", "Transcriptome Analysis", "Gene expression data from short term in vivo studies shows efficacy in quantifying concentration dependent effects that inform toxicity outcomes  particularly for chemicals with limited toxicity data such as Per  and Polyfluoroalkyl Substances PFAS. Automated behavioral assessments  at non teratogenic concentrations reveal perfluorohexane 1 sulfonate PFHxS exposure causes hyperactivity in larval zebrafish 6 dpf dpf during the light phase of the light:dark assay compared to 0.4% dimethylsulfoxide DMSO vehicle control. To identify key events that drive this abnormal behavior  zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO  and RNA was isolated from pooled head tissue collected at 4 dpf and 5 dpf  before the onset of hyperactivity  for RNA sequencing NextSeq 500. Differentially expressed genes DEGs were identified using Gene Specific Analysis Partek Flow  St. Louis  MO and mapped to human orthologs for pathway analyses to inform modes of action. Overall design: At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u00b5m nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u00b5L of 10% Hanks' balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u00b5L of 10% HBSS Westerfield 2007 and 1\u00b5L of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u00b5M PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", null, null, null, "GRC350 D5 3F S10", "GSM5711819", null, "tissue:pooled heads collected anterior to swim bladder|treatment:potassium perfluorohexane 1 sulfonate|age:5 dpf stage:larvae|strain:mixed wildtype", "GRC350 D5 3F S10", "Fastq files were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow v.8.0.19.0428; St. Louis  MO. Gene counts were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation Gene features were offset to 0.0001 and those with geometric means across all samples \u2264 1 were filtered Sample gene counts were quantile normalized and log2 transformed Genome build: GRCz11 Ensembl version 93 gene annotation build Supplementary files format and content: tab delimited  raw gene count matrix  normalized gene count matrix", "pooled heads collected anterior to swim bladder", "At 0 dpf  zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 \u03bcm nylon mesh filter Millipore  Catalog No. MANMN4010 with 400\u03bcL of 10% Hanks\u2019 balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore  Catalog No. MAMCS9610 containing 250\u03bcL of 10% HBSS Westerfield 2007 and 1\u03bcL of 250\u00d7 working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily  from 1\u20134 or 1 dpf 5 dpf  plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation  plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0\u00b0C and scored daily for death  malformations  hatching  and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 \u03bcM PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "All procedures involving zebrafish were approved by the U.S. Environmental Protection Agency EPA National Health and Environmental Effects Research Laboratory Institutional Animal Care and Use Committee and carried out in accordance with the relevant guidelines and regulations. Embryos were obtained from a mixed wild type WT adult zebrafish line Danio rerio that was generated and maintained as previously described Phelps et al. 2017. Briefly  to maintain genetic diversity  a minimum of one WT line AB and/or Tupfel long fin WT strains was added one time per year. Zebrafish adults were housed in 6 L tanks at an approximate density of 8\u2009fish/L. Adults were fed Gemma Micro 300 Skretting once daily and shell free E Z Egg Brine Shrimp Direct twice daily Mondays through Fridays. Both food sources were fed once daily on weekends. U.S. EPA WT zebrafish were maintained on a 14 h:10 h light cycle at 28.5\u00b0C and bred every 2\u20133 weeks. For embryo collection  60\u2013100 adults were placed in 10  or 20 L angled static breeding tanks overnight. The following morning  adults were transferred to new angled bottom tanks containing fish facility water  and embryos were collected 30\u201340 min later.", "treatment:potassium perfluorohexane 1 sulfonate|concentration \u00b5m:7.87|age:5 dpf stage:larvae|strain:mixed wildtype", "GSM5711819", "GSM5711819: GRC350 D5 3F S10; Danio rerio; RNA Seq", "GSM5711819", null, "1", "Each pooled sample underwent RNA extraction using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS  the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix  and they were run for 75 cycles single read.", "GEO Accession:GSM5711819", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP348912", null, null, "GRC350-D5-3F_S10_L001_R1_001.fastq.gz", "fastq", 453579975.0, 6047733.0, "GSM5711819 r1", "0:75 1:0", "A:120833503;C:101700505;G:110413638;T:120555105;N:77224", 75, 0, null, null, 120833503, 101700505, 110413638, 120555105, 77224, "SRX13284816", "SRS11197573", "SRA1337575", "GEO", "US EPA", 1, 0.94667, null, 0.09349, null, 0.70676, null, 0.47641, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2021-12-02", "Larval", "Larval", "Multi-tissue", "Multi-system"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["67133"], "units": {}, "query_ms": 12.531758009572513}